Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/df28f039abaf5d3aa46f3fa733644f/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/df28f039abaf5d3aa46f3fa733644f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_KFJ-N1-BDNA-1_B23L5TMLT4_1/1029_KFJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_KFJ-N1-BDNA-1_B23L5TMLT4_1/1029_KFJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_KFJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KFJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KFJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_KFJ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 15256668 total, 18617 skipped (flags/unmapped)
Fragments: 7851361 total (7379726 tlen-paired, 1435 hash-paired, 131 singletons, 1243 discordant, 468826 orphans, 2143 too large [>5000 bp], 3354679 duplicates)
Reads: 16132360 total, 18305 skipped (flags/unmapped)
Fragments: 8306519 total (7799305 tlen-paired, 1433 hash-paired, 147 singletons, 1010 discordant, 504624 orphans, 2894 too large [>5000 bp], 3451414 duplicates)
Reads: 16117318 total, 17071 skipped (flags/unmapped)
Fragments: 8296699 total (7794073 tlen-paired, 1731 hash-paired, 106 singletons, 1202 discordant, 499587 orphans, 3271 too large [>5000 bp], 3535632 duplicates)
Reads: 19629310 total, 37433 skipped (flags/unmapped)
Fragments: 10367879 total (8530126 tlen-paired, 1412 hash-paired, 149 singletons, 381182 discordant, 1455010 orphans, 155639 too large [>5000 bp], 4077044 duplicates)